5ysp: Difference between revisions

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'''Unreleased structure'''


The entry 5ysp is ON HOLD  until Paper Publication
==Pyrophosphate-dependent kinase in the ribokinase family complexed with a pyrophosphate analog and myo-inositol==
<StructureSection load='5ysp' size='340' side='right' caption='[[5ysp]], [[Resolution|resolution]] 1.70&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[5ysp]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5YSP OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5YSP FirstGlance]. <br>
</td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=INS:1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE'>INS</scene>, <scene name='pdbligand=MDN:METHYLENEDIPHOSPHONIC+ACID'>MDN</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</scene></td></tr>
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5ysp FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5ysp OCA], [http://pdbe.org/5ysp PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5ysp RCSB], [http://www.ebi.ac.uk/pdbsum/5ysp PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5ysp ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
Almost all kinases utilize ATP as their phosphate donor, while a few kinases utilize pyrophosphate (PPi) instead. PPi-dependent kinases are often homologous to their ATP-dependent counterparts, but determinants of their different donor specificities remain unclear. We identify a PPi-dependent member of the ribokinase family, which differs from known PPi-dependent kinases, and elucidate its PPi-binding mode based on the crystal structures. Structural comparison and sequence alignment reveal five important residues: three basic residues specifically recognizing PPi and two large hydrophobic residues occluding a part of the ATP-binding pocket. Two of the three basic residues adapt a conserved motif of the ribokinase family for the PPi binding. Using these five key residues as a signature pattern, we discover additional PPi-specific members of the ribokinase family, and thus conclude that these residues are the determinants of PPi-specific binding. Introduction of these residues may enable transformation of ATP-dependent ribokinase family members into PPi-dependent enzymes.


Authors: Nagata, R., Fujihashi, M., Miki, K.
Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants.,Nagata R, Fujihashi M, Sato T, Atomi H, Miki K Nat Commun. 2018 May 2;9(1):1765. doi: 10.1038/s41467-018-04201-z. PMID:29720581<ref>PMID:29720581</ref>


Description: Pyrophosphate-dependent kinase in the ribokinase family complexed with a pyrophosphate analog and myo-inositol
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
[[Category: Unreleased Structures]]
</div>
<div class="pdbe-citations 5ysp" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Fujihashi, M]]
[[Category: Fujihashi, M]]
[[Category: Miki, K]]
[[Category: Nagata, R]]
[[Category: Nagata, R]]
[[Category: Miki, K]]
[[Category: Transferase]]
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